devel/doxygen: 1.8.3.1 -> 1.8.7

In a second step, the python build part has to be tested (still open)

PR:		ports/190943
Submitted by:	Naram Qashat <cyberbotx@cyberbotx.com> (maintainer)

19 files changed, 390 insertions, 298 deletions

diff --git a/devel/doxygen/Makefile b/devel/doxygen/Makefile
index 5f1233a47c42..047c03c76f23 100644
--- a/devel/doxygen/Makefile
+++ b/devel/doxygen/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	doxygen
-PORTVERSION=	1.8.3.1
-PORTREVISION=	1
+PORTVERSION=	1.8.7
 CATEGORIES=	devel
 MASTER_SITES=	ftp://ftp.stack.nl/pub/users/dimitri/ \
 		http://ftp.stack.nl/pub/users/dimitri/
@@ -15,15 +14,18 @@ COMMENT=	Documentation system for C, C++, and other languages
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BUILD_DEPENDS=	tmake:${PORTSDIR}/devel/tmake
-LIB_DEPENDS=	png15:${PORTSDIR}/graphics/png
+BUILD_DEPENDS=	tmake:${PORTSDIR}/devel/tmake \
+		flex>0:${PORTSDIR}/textproc/flex \
+		python:${PORTSDIR}/lang/python
+LIB_DEPENDS=	libpng15.so:${PORTSDIR}/graphics/png
 
 USES=		bison iconv perl5 gmake
 ALL_TARGET=	all
 HAS_CONFIGURE=	yes
+MAKE_JOBS_UNSAFE=	yes
 QT_NONSTANDARD=	yes	# non-standard configure arguments
 CONFIGURE_ARGS=	--prefix ${PREFIX} --perl ${PERL} --make ${GMAKE} \
-		--install "${INSTALL}"
+		--install "${INSTALL}" --flex ${LOCALBASE}/bin/flex
 REINPLACE_ARGS=	-i ''
 
 EXTRACT_AFTER_ARGS=	--exclude '*/libmd5'	\
diff --git a/devel/doxygen/distinfo b/devel/doxygen/distinfo
index e1689347233b..550afd722a04 100644
--- a/devel/doxygen/distinfo
+++ b/devel/doxygen/distinfo
@@ -1,2 +1,2 @@
-SHA256 (doxygen-1.8.3.1.src.tar.gz) = 0c749f68101b6c04ccb0d9696dd37836a6ba62cd8002add275058a975ee72b55
-SIZE (doxygen-1.8.3.1.src.tar.gz) = 6196887
+SHA256 (doxygen-1.8.7.src.tar.gz) = c6eac6b6e82148ae15ec5aecee4631547359f284af1ce94474d046ebca6ee3d9
+SIZE (doxygen-1.8.7.src.tar.gz) = 4796875
diff --git a/devel/doxygen/files/patch-Makefile.in b/devel/doxygen/files/patch-Makefile.in
new file mode 100644
index 000000000000..7eb985013d0e
--- /dev/null
+++ b/devel/doxygen/files/patch-Makefile.in
@@ -0,0 +1,49 @@
+--- Makefile.in-orig	2014-06-14 08:30:10.000000000 +0200
++++ Makefile.in	2014-06-14 08:31:21.000000000 +0200
+@@ -16,11 +16,10 @@
+ 	cd addon/doxyapp ; $(MAKE) clean
+ 
+ clean: FORCE
+-	- cd examples ; $(MAKE) clean
+-	- cd doc ; $(MAKE) clean
+-	- cd qtools ; $(MAKE) clean
+-	- cd src ; $(MAKE) clean
+-	- cd libmd5 ; $(MAKE) clean
++	-cd examples ; $(MAKE) clean
++	-cd doc ; $(MAKE) clean
++	-cd qtools ; $(MAKE) clean
++	-cd src ; $(MAKE) clean
+ 	-cd addon/doxywizard ; $(MAKE) clean
+ 	-cd addon/doxysearch ; $(MAKE) clean
+ 	-cd addon/doxyapp ; $(MAKE) clean
+@@ -32,7 +31,6 @@
+ 
+ distclean: clean
+ 	-cd src ; $(MAKE) distclean
+-	-cd libmd5 ; $(MAKE) distclean
+ 	-cd addon/doxywizard ; $(MAKE) distclean
+ 	-cd addon/doxysearch ; $(MAKE) distclean
+ 	-cd addon/doxyapp ; $(MAKE) distclean
+@@ -51,9 +49,8 @@
+ 	-rm -rf xml
+ 	-rm -f src/Makefile.doxygen src/Makefile.libdoxygen 
+ 	-rm -f src/Makefile.libdoxycfg src/libdoxycfg.t src/libdoxygen.t
+-	-rm -f libmd5/Makefile.libmd5
+ 	-rm -f .makeconfig .tmakeconfig
+-	-rm -f src/doxygen.pro src/libdoxygen.pro qtools/qtools.pro src/libdoxycfg.pro libmd5/libmd5.pro
++	-rm -f src/doxygen.pro src/libdoxygen.pro qtools/qtools.pro src/libdoxycfg.pro
+ 	-rm -rf generated_src
+ 	-rm -f addon/doxywizard/doxywizard.pro
+ 	-rm -f VERSION
+@@ -93,9 +90,9 @@
+ 	cd doc ; $(MAKE)
+ 
+ pdf: docs
+-	cd latex ; $(MAKE)
++	cd latex ; patch < ../refman-patch ; patch < ../latex-patch ; $(MAKE)
+ 
+-DISTFILES =  Doxyfile libmd5 addon tmake doc examples bin lib objects testing \
++DISTFILES =  Doxyfile addon tmake doc examples bin lib objects testing \
+              qtools src configure configure.bin Makefile.in Makefile.win_nmake.in \
+              Makefile.win_make.in INSTALL LANGUAGE.HOWTO LICENSE PLATFORMS \
+              VERSION README.md packages winbuild jquery
diff --git a/devel/doxygen/files/patch-addon-doxywizard-Makefile.in b/devel/doxygen/files/patch-addon-doxywizard-Makefile.in
index 8f017b9283ba..056ffaf79939 100644
--- a/devel/doxygen/files/patch-addon-doxywizard-Makefile.in
+++ b/devel/doxygen/files/patch-addon-doxywizard-Makefile.in
@@ -1,11 +1,11 @@
---- addon/doxywizard/Makefile.in.orig	2010-05-23 10:51:31.000000000 -0400
-+++ addon/doxywizard/Makefile.in	2010-06-15 07:44:44.000000000 -0400
+--- addon/doxywizard/Makefile.in-orig	2014-06-13 23:29:16.000000000 +0200
++++ addon/doxywizard/Makefile.in	2014-06-13 23:28:50.000000000 +0200
 @@ -10,7 +10,7 @@
  # See the GNU General Public License for more details.
  # 
  
--QMAKE=qmake $(MKSPECS)
-+QMAKE=qmake-qt4 $(MKSPECS)
+-QMAKE=$(QTDIR)/bin/qmake $(MKSPECS)
++QMAKE=$(QTDIR)/bin/qmake-qt4 $(MKSPECS)
+ INCBUFSIZE=$(PYTHON) ../../src/increasebuffer.py
  
  all: Makefile.doxywizard  
- 	$(MAKE) -f Makefile.doxywizard 
diff --git a/devel/doxygen/files/patch-ah b/devel/doxygen/files/patch-ah
deleted file mode 100644
index 806a0c312983..000000000000
--- a/devel/doxygen/files/patch-ah
+++ /dev/null
@@ -1,21 +0,0 @@
---- doc/doxygen_manual.tex.orig	2012-02-11 18:34:00.000000000 -0500
-+++ doc/doxygen_manual.tex	2012-03-04 13:56:33.000000000 -0500
-@@ -13,7 +13,7 @@
- % input used in their production; they are not affected by this license.
- 
- \documentclass{book}
--\usepackage[a4paper,left=2.5cm,right=2.5cm,top=2.5cm,bottom=2.5cm]{geometry}
-+\usepackage[left=2.5cm,right=2.5cm,top=2.5cm,bottom=2.5cm]{geometry}
- \usepackage{makeidx}
- \usepackage{natbib}
- \usepackage{graphicx}
-@@ -28,8 +28,7 @@
- \usepackage{alltt}
- \usepackage{ifpdf}
- \ifpdf
--\usepackage[pdftex,
--            pagebackref=true,
-+\usepackage[pagebackref=true,
-             colorlinks=true,
-             linkcolor=blue,
-             unicode
diff --git a/devel/doxygen/files/patch-configure b/devel/doxygen/files/patch-configure
index 2127793aa43c..7994ac79ad0e 100644
--- a/devel/doxygen/files/patch-configure
+++ b/devel/doxygen/files/patch-configure
@@ -1,15 +1,28 @@
---- configure.orig	2012-12-27 06:24:51.000000000 -0500
-+++ configure	2012-12-28 12:12:33.000000000 -0500
-@@ -281,7 +281,7 @@
+--- configure.orig	2014-04-20 17:17:29.000000000 +0200
++++ configure	2014-06-13 23:25:23.000000000 +0200
+@@ -363,25 +363,25 @@
      echo "  QTDIR environment variable not set!"
-     echo -n "  Checking for Qt..."
+     printf "  Checking for Qt..."
      for d in /usr/{lib,share,qt}/{qt-4,qt4,qt,qt*,4} /usr; do
 -      if test -x "$d/bin/qmake"; then
 +      if test -x "$d/bin/qmake-qt4"; then
          QTDIR=$d
+         break 2
        fi
      done
-@@ -292,7 +292,7 @@
+   else
+-    if test -e "$QTDIR/bin/qmake"; then
++    if test -e "$QTDIR/bin/qmake-qt4"; then
+       printf "  Detected Qt via the QTDIR environment variable..."
+     else
+       printf "ERROR Detected Qt via the QTDIR environment variable..."
+-      echo ", but $QTDIR/bin/qmake does not exist."
+-      echo "      Set the QTDIR environment variable such that \$QTDIR/bin/qmake exists."
++      echo ", but $QTDIR/bin/qmake-qt4 does not exist."
++      echo "      Set the QTDIR environment variable such that \$QTDIR/bin/qmake-qt4 exists."
+       exit 2
+     fi
+   fi
    if test -z "$QTDIR"; then
      echo "QTDIR not set and Qt not found at standard locations!"
      echo
@@ -18,7 +31,7 @@
      echo "check the Qt installation instructions!"
      exit 2
    fi
-@@ -604,7 +604,7 @@
+@@ -848,7 +848,7 @@
  fi
  if test "$f_wizard" = YES; then
    cat >> .tmakeconfig <<EOF
@@ -27,7 +40,7 @@
  EOF
  fi
  
-@@ -621,7 +621,7 @@
+@@ -859,7 +859,7 @@
  EOF
  fi
  
@@ -36,17 +49,17 @@
  
  for i in $f_inmakefiles ; do
       SRC=$i
-@@ -645,7 +645,6 @@
-        fi
-        echo "all: src/version.cpp $EXTRADEPS" >> $DST
+@@ -883,7 +883,6 @@
+ #       fi
+        echo "all: generated_src/doxygen/version.cpp $EXTRADEPS" >> $DST
         echo "	\$(MAKE) -C qtools" >> $DST
 -       echo "	\$(MAKE) -C libmd5" >> $DST
         echo "	\$(MAKE) -C src" >> $DST
         if test $f_wizard = YES; then
           echo "	\$(MAKE) MAN1DIR=\$(MAN1DIR) -C addon/doxywizard" >> $DST
-@@ -678,7 +677,7 @@
- cat src/libdoxycfg.t.in | sed -e "s|%%FLEX%%|$f_flex|g" -e "s|%%BISON%%|$f_bison|g" > src/libdoxycfg.t
- cat src/libdoxygen.t.in | sed -e "s|%%FLEX%%|$f_flex|g" -e "s|%%BISON%%|$f_bison|g" > src/libdoxygen.t
+@@ -921,7 +920,7 @@
+ cat src/libdoxycfg.t.in | sed -e "s|%%FLEX%%|$f_flex|g" -e "s|%%BISON%%|$f_bison|g" -e "s|%%PYTHON%%|$f_python|g" > src/libdoxycfg.t
+ cat src/libdoxygen.t.in | sed -e "s|%%FLEX%%|$f_flex|g" -e "s|%%BISON%%|$f_bison|g" -e "s|%%PYTHON%%|$f_python|g" > src/libdoxygen.t
  
 -f_inprofiles="qtools/qtools.pro.in src/libdoxygen.pro.in src/libdoxycfg.pro.in src/doxygen.pro.in addon/doxywizard/doxywizard.pro.in addon/doxmlparser/src/doxmlparser.pro.in addon/doxmlparser/test/xmlparse.pro.in addon/doxmlparser/examples/metrics/metrics.pro.in libmd5/libmd5.pro.in addon/doxyapp/doxyapp.pro.in addon/doxysearch/doxysearch.pro.in addon/doxysearch/doxyindexer.pro.in" 
 +f_inprofiles="qtools/qtools.pro.in src/libdoxygen.pro.in src/libdoxycfg.pro.in src/doxygen.pro.in addon/doxywizard/doxywizard.pro.in addon/doxmlparser/src/doxmlparser.pro.in addon/doxmlparser/test/xmlparse.pro.in addon/doxmlparser/examples/metrics/metrics.pro.in addon/doxyapp/doxyapp.pro.in addon/doxysearch/doxysearch.pro.in addon/doxysearch/doxyindexer.pro.in" 
diff --git a/devel/doxygen/files/patch-examples-Makefile.in b/devel/doxygen/files/patch-examples-Makefile.in
deleted file mode 100644
index 628300a0319f..000000000000
--- a/devel/doxygen/files/patch-examples-Makefile.in
+++ /dev/null
@@ -1,16 +0,0 @@
-Disables tests to avoid hang on stable/9 and head.
-
-Temporary fix until correct solution is found.
-
-
-Index: examples/Makefile.in
-@@ -124,7 +124,7 @@
- #	$(DOXYGEN)/bin/doxygen dbusxml.cfg
- 
- diagrams/html/index.html: diagrams_a.h diagrams_b.h diagrams_c.h diagrams_d.h diagrams_e.h diagrams.cfg
--ifneq ($(HAVE_DOT),)
--	$(DOXYGEN)/bin/doxygen diagrams.cfg
--endif
-+#ifneq ($(HAVE_DOT),)
-+#	$(DOXYGEN)/bin/doxygen diagrams.cfg
-+#endif
diff --git a/devel/doxygen/files/patch-latex b/devel/doxygen/files/patch-latex
new file mode 100644
index 000000000000..8c96a67b7322
--- /dev/null
+++ b/devel/doxygen/files/patch-latex
@@ -0,0 +1,30 @@
+--- latex-patch.orig	1970-01-01 01:00:00.000000000 +0100
++++ latex-patch	2014-06-13 23:18:40.000000000 +0200
+@@ -0,0 +1,27 @@
++--- Makefile.orig	2014-06-13 23:14:28.000000000 +0200
+++++ Makefile	2014-06-13 23:18:27.000000000 +0200
++@@ -3,19 +3,19 @@
++ pdf: refman.pdf
++ 
++ refman.pdf: clean refman.tex
++-	pdflatex refman
+++	-pdflatex -interaction nonstopmode refman
++ 	makeindex refman.idx
++-	pdflatex refman
+++	-pdflatex -interaction nonstopmode refman
++ 	latex_count=8 ; \
++ 	while egrep -s 'Rerun (LaTeX|to get cross-references right)' refman.log && [ $$latex_count -gt 0 ] ;\
++ 	    do \
++ 	      echo "Rerunning latex...." ;\
++-	      pdflatex refman ;\
+++	      pdflatex -interaction nonstopmode refman ;\
++ 	      latex_count=`expr $$latex_count - 1` ;\
++ 	    done
++ 	makeindex refman.idx
++-	pdflatex refman
++-
+++	-pdflatex -interaction nonstopmode refman
+++	cp refman.pdf doxygen_manual.pdf
++ 
++ clean:
++ 	rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl refman.pdf
diff --git a/devel/doxygen/files/patch-md5 b/devel/doxygen/files/patch-md5
deleted file mode 100644
index 5474f0f4d0e2..000000000000
--- a/devel/doxygen/files/patch-md5
+++ /dev/null
@@ -1,221 +0,0 @@
---- src/definition.cpp.orig	2011-08-19 15:34:17.000000000 +0800
-+++ src/definition.cpp	2011-10-31 17:32:47.870380518 +0800
-@@ -18,6 +18,7 @@
- #include "qtbc.h"
- #include <ctype.h>
- #include <qregexp.h>
-+#include <sys/types.h>
- #include "md5.h"
- #include <stdio.h>
- #include <stdlib.h>
-@@ -361,13 +362,11 @@
- 
- bool Definition::_docsAlreadyAdded(const QCString &doc)
- {
--  uchar md5_sig[16];
-   QCString sigStr(33);
-   // to avoid mismatches due to differences in indenting, we first remove
-   // double whitespaces...
-   QCString docStr = doc.simplifyWhiteSpace();
--  MD5Buffer((const unsigned char *)docStr.data(),docStr.length(),md5_sig);
--  MD5SigToString(md5_sig,sigStr.data(),33);
-+  MD5Data((const unsigned char *)docStr.data(),docStr.length(),sigStr.data());
-   if (m_impl->docSignatures.find(sigStr)==-1) // new docs, add signature to prevent re-adding it
-   {
-     m_impl->docSignatures+=":"+sigStr;
---- src/dirdef.cpp.orig	2011-07-26 19:54:31.000000000 +0800
-+++ src/dirdef.cpp	2011-10-31 17:32:47.872380214 +0800
-@@ -1,3 +1,4 @@
-+#include <sys/types.h>
- #include "md5.h"
- 
- #include "dirdef.h"
-@@ -75,10 +76,8 @@
-   QCString result;
- 
-   // convert to md5 hash
--  uchar md5_sig[16];
-   QCString sigStr(33);
--  MD5Buffer((const unsigned char *)anchor.data(),anchor.length(),md5_sig);
--  MD5SigToString(md5_sig,sigStr.data(),33);
-+  MD5Data((const unsigned char *)anchor.data(),anchor.length(),sigStr.data());
-   return sigStr;
- 
-   // old algorithm
---- src/dot.cpp.orig	2011-08-09 02:06:19.000000000 +0800
-+++ src/dot.cpp	2011-10-31 17:32:47.877389789 +0800
-@@ -39,6 +39,7 @@
- #include <qdir.h>
- #include <qfile.h>
- #include "ftextstream.h"
-+#include <sys/types.h>
- #include "md5.h"
- #include <qqueue.h>
- 
-@@ -2063,10 +2064,8 @@
-     }
-     writeGraphFooter(md5stream);
-     resetReNumbering();
--    uchar md5_sig[16];
-     QCString sigStr(33);
--    MD5Buffer((const unsigned char *)theGraph.data(),theGraph.length(),md5_sig);
--    MD5SigToString(md5_sig,sigStr.data(),33);
-+    MD5Data((const unsigned char *)theGraph.data(),theGraph.length(),sigStr.data());
-     bool regenerate=FALSE;
-     if (checkAndUpdateMd5Signature(absBaseName,sigStr) || 
-         !checkDeliverables(absImgName,absMapName))
-@@ -2758,10 +2757,8 @@
-     }
-   }
-   writeGraphFooter(md5stream);
--  uchar md5_sig[16];
-   QCString sigStr(33);
--  MD5Buffer((const unsigned char *)buf.data(),buf.length(),md5_sig);
--  MD5SigToString(md5_sig,sigStr.data(),33);
-+  MD5Data((const unsigned char *)buf.data(),buf.length(),sigStr.data());
-   if (reNumber)
-   {
-     resetReNumbering();
-@@ -3609,10 +3606,8 @@
-   QGString theGraph;
-   FTextStream md5stream(&theGraph);
-   m_dir->writeDepGraph(md5stream);
--  uchar md5_sig[16];
-   QCString sigStr(33);
--  MD5Buffer((const unsigned char *)theGraph.data(),theGraph.length(),md5_sig);
--  MD5SigToString(md5_sig,sigStr.data(),33);
-+  MD5Data((const unsigned char *)theGraph.data(),theGraph.length(),sigStr.data());
-   bool regenerate=FALSE;
-   if (checkAndUpdateMd5Signature(absBaseName,sigStr) ||
-       !checkDeliverables(format==BITMAP ? absImgName :
-@@ -3739,10 +3734,8 @@
-   md5stream << "  Node18 -> Node9 [dir=\"back\",color=\"darkorchid3\",fontsize=\"" << FONTSIZE << "\",style=\"dashed\",label=\"m_usedClass\",fontname=\"" << FONTNAME << "\"];\n";
-   md5stream << "  Node18 [shape=\"box\",label=\"Used\",fontsize=\"" << FONTSIZE << "\",height=0.2,width=0.4,fontname=\"" << FONTNAME << "\",color=\"black\",URL=\"$classUsed" << Doxygen::htmlFileExtension << "\"];\n";
-   writeGraphFooter(md5stream);
--  uchar md5_sig[16];
-   QCString sigStr(33);
--  MD5Buffer((const unsigned char *)theGraph.data(),theGraph.length(),md5_sig);
--  MD5SigToString(md5_sig,sigStr.data(),33);
-+  MD5Data((const unsigned char *)theGraph.data(),theGraph.length(),sigStr.data());
-   QCString absBaseName = (QCString)path+"/graph_legend";
-   QCString absDotName  = absBaseName+".dot";
-   QCString imgExt      = Config_getEnum("DOT_IMAGE_FORMAT");
-@@ -4139,10 +4132,8 @@
- 
-   writeGraphFooter(md5stream);
-   resetReNumbering();
--  uchar md5_sig[16];
-   QCString sigStr(33);
--  MD5Buffer((const unsigned char *)theGraph.data(),theGraph.length(),md5_sig);
--  MD5SigToString(md5_sig,sigStr.data(),33);
-+  MD5Data((const unsigned char *)theGraph.data(),theGraph.length(),sigStr.data());
-   QCString imgExt      = Config_getEnum("DOT_IMAGE_FORMAT");
-   QCString baseName    = m_diskName;
-   QCString imgName     = baseName+"."+imgExt;
---- src/doxygen.pro.in.orig	2011-01-04 04:14:46.000000000 +0800
-+++ src/doxygen.pro.in	2011-10-31 17:32:47.879381383 +0800
-@@ -18,7 +18,7 @@
- CONFIG       =	console warn_on $extraopts
- HEADERS      =	doxygen.h 
- SOURCES      =	main.cpp 
--unix:LIBS                  += -L../lib -ldoxygen -ldoxycfg -lqtools -lmd5 -lpthread
-+unix:LIBS                  += -L../lib -ldoxygen -ldoxycfg -lqtools -lmd -lpthread
- win32:INCLUDEPATH          += .
- win32-mingw:LIBS           += -L../lib -ldoxygen -ldoxycfg -lqtools -lmd5 -lpthread
- win32-msvc:LIBS            += qtools.lib md5.lib doxygen.lib doxycfg.lib shell32.lib iconv.lib
-@@ -28,7 +28,7 @@
- win32:TMAKE_CXXFLAGS       += -DQT_NODLL
- win32-g++:LIBS             = -L../lib -ldoxygen -ldoxycfg -lqtools -lmd5 -liconv -lpthread
- win32-g++:TMAKE_CXXFLAGS   += -fno-exceptions -fno-rtti
--INCLUDEPATH                += ../qtools ../libmd5 .
-+INCLUDEPATH                += ../qtools .
- DESTDIR                    =  ../bin
- TARGET                     =  doxygen
- unix:TARGETDEPS            =  ../lib/libdoxygen.a ../lib/libdoxycfg.a
---- src/memberdef.cpp.orig	2011-08-18 22:46:40.000000000 +0800
-+++ src/memberdef.cpp	2011-10-31 17:35:14.027187598 +0800
-@@ -19,6 +19,7 @@
- #include <qglobal.h>
- #include <qregexp.h>
- #include <assert.h>
-+#include <sys/types.h>
- #include "md5.h"
- #include "memberdef.h"
- #include "membername.h"
-@@ -2771,11 +2772,9 @@
-   }
-   
-   // convert to md5 hash
--  uchar md5_sig[16];
-   QCString sigStr(33);
--  MD5Buffer((const unsigned char *)memAnchor.data(),memAnchor.length(),md5_sig);
-+  MD5Data((const unsigned char *)memAnchor.data(),memAnchor.length(),sigStr.data());
-   //printf("memAnchor=%s\n",memAnchor.data());
--  MD5SigToString(md5_sig,sigStr.data(),33);
-   m_impl->anc = "a"+sigStr;
- }
- 
---- src/membergroup.cpp.orig	2011-04-22 18:08:07.000000000 +0800
-+++ src/membergroup.cpp	2011-10-31 17:32:47.886381993 +0800
-@@ -265,12 +265,10 @@
- 
- QCString MemberGroup::anchor() const
- {
--  uchar md5_sig[16];
-   QCString sigStr(33);
-   QCString locHeader = grpHeader;
-   if (locHeader.isEmpty()) locHeader="[NOHEADER]";
--  MD5Buffer((const unsigned char *)locHeader.data(),locHeader.length(),md5_sig);
--  MD5SigToString(md5_sig,sigStr.data(),33);
-+  MD5Data((const unsigned char *)locHeader.data(),locHeader.length(),sigStr.data());
-   return "amgrp"+sigStr;
- }
- 
---- src/util.cpp.orig	2011-08-19 23:11:12.000000000 +0800
-+++ src/util.cpp	2011-10-31 17:32:47.892382197 +0800
-@@ -20,6 +20,7 @@
- #include <errno.h>
- #include <math.h>
- 
-+#include <sys/types.h>
- #include "md5.h"
- 
- #include "qtbc.h"
-@@ -4901,16 +4902,16 @@
-     if (resultLen>=128) // prevent names that cannot be created!
-     {
-       // third algorithm based on MD5 hash
--      uchar md5_sig[16];
-       QCString sigStr(33);
--      MD5Buffer((const unsigned char *)result.data(),resultLen,md5_sig);
--      MD5SigToString(md5_sig,sigStr.data(),33);
-+      MD5Data((const unsigned char *)result.data(),resultLen,sigStr.data());
-       result=result.left(128-32)+sigStr; 
-     }
-   }
-   if (createSubdirs)
-   {
-+#if MAP_ALGO==ALGO_COUNT || MAP_ALGO==ALGO_CRC16
-     int l1Dir=0,l2Dir=0;
-+#endif
- 
- #if MAP_ALGO==ALGO_COUNT 
-     // old algorithm, has the problem that after regeneration the
-@@ -4941,12 +4942,13 @@
-     l2Dir = (dirNum>>4)&0xff;
- #elif MAP_ALGO==ALGO_MD5
-     // third algorithm based on MD5 hash
--    uchar md5_sig[16];
--    MD5Buffer((const unsigned char *)result.data(),result.length(),md5_sig);
--    l1Dir = md5_sig[14]&0xf;
--    l2Dir = md5_sig[15];
-+    char md5[33];
-+    MD5Data((const unsigned char *)result.data(),result.length(),md5);
-+    result.prepend(QCString().sprintf("d%c/d%c%c/",md5[29],md5[30],md5[31]));
- #endif
-+#if MAP_ALGO==ALGO_COUNT || MAP_ALGO==ALGO_CRC16
-     result.prepend(QCString().sprintf("d%x/d%02x/",l1Dir,l2Dir));
-+#endif
-   }
-   //printf("*** convertNameToFile(%s)->%s\n",name,result.data());
-   return result;
diff --git a/devel/doxygen/files/patch-md5-Doxyfile b/devel/doxygen/files/patch-md5-Doxyfile
new file mode 100644
index 000000000000..3eba034fac40
--- /dev/null
+++ b/devel/doxygen/files/patch-md5-Doxyfile
@@ -0,0 +1,11 @@
+--- Doxyfile.orig	2014-06-14 08:11:43.000000000 +0200
++++ Doxyfile	2014-06-14 08:11:47.000000000 +0200
+@@ -257,7 +257,7 @@
+ MACRO_EXPANSION        = YES
+ EXPAND_ONLY_PREDEF     = YES
+ SEARCH_INCLUDES        = YES
+-INCLUDE_PATH           = qtools libmd5
++INCLUDE_PATH           = qtools
+ INCLUDE_FILE_PATTERNS  =
+ PREDEFINED             =
+ EXPAND_AS_DEFINED      =
diff --git a/devel/doxygen/files/patch-md5-definition b/devel/doxygen/files/patch-md5-definition
new file mode 100644
index 000000000000..f2e84bf63150
--- /dev/null
+++ b/devel/doxygen/files/patch-md5-definition
@@ -0,0 +1,25 @@
+--- src/definition.cpp-orig	2014-06-11 20:09:07.000000000 +0200
++++ src/definition.cpp	2014-06-11 20:12:32.000000000 +0200
+@@ -17,6 +17,7 @@
+ 
+ #include <ctype.h>
+ #include <qregexp.h>
++#include <sys/types.h>
+ #include "md5.h"
+ #include <stdio.h>
+ #include <stdlib.h>
+@@ -539,13 +540,11 @@
+ 
+ bool Definition::_docsAlreadyAdded(const QCString &doc,QCString &sigList)
+ {
+-  uchar md5_sig[16];
+   QCString sigStr(33);
+   // to avoid mismatches due to differences in indenting, we first remove
+   // double whitespaces...
+   QCString docStr = doc.simplifyWhiteSpace();
+-  MD5Buffer((const unsigned char *)docStr.data(),docStr.length(),md5_sig);
+-  MD5SigToString(md5_sig,sigStr.data(),33);
++  MD5Data((const unsigned char *)docStr.data(),docStr.length(),sigStr.data());
+   //printf("%s:_docsAlreadyAdded doc='%s' sig='%s' docSigs='%s'\n",
+   //    name().data(),doc.data(),sigStr.data(),sigList.data());
+   if (sigList.find(sigStr)==-1) // new docs, add signature to prevent re-adding it
diff --git a/devel/doxygen/files/patch-md5-dirdef b/devel/doxygen/files/patch-md5-dirdef
new file mode 100644
index 000000000000..5789af46e2fa
--- /dev/null
+++ b/devel/doxygen/files/patch-md5-dirdef
@@ -0,0 +1,19 @@
+--- src/dirdef.cpp-orig	2014-06-11 20:11:16.000000000 +0200
++++ src/dirdef.cpp	2014-06-11 20:11:59.000000000 +0200
+@@ -1,3 +1,4 @@
++#include <sys/types.h>
+ #include "md5.h"
+ 
+ #include "dirdef.h"
+@@ -83,10 +84,8 @@
+   QCString result;
+ 
+   // convert to md5 hash
+-  uchar md5_sig[16];
+   QCString sigStr(33);
+-  MD5Buffer((const unsigned char *)anchor.data(),anchor.length(),md5_sig);
+-  MD5SigToString(md5_sig,sigStr.data(),33);
++  MD5Data((const unsigned char *)anchor.data(),anchor.length(),sigStr.data());
+   return sigStr;
+ 
+   // old algorithm
diff --git a/devel/doxygen/files/patch-md5-dot b/devel/doxygen/files/patch-md5-dot
new file mode 100644
index 000000000000..d833f4a9059d
--- /dev/null
+++ b/devel/doxygen/files/patch-md5-dot
@@ -0,0 +1,70 @@
+--- src/dot.cpp-orig	2014-06-11 20:13:39.000000000 +0200
++++ src/dot.cpp	2014-06-11 20:15:32.000000000 +0200
+@@ -44,6 +44,7 @@
+ #include "dirdef.h"
+ #include "vhdldocgen.h"
+ #include "ftextstream.h"
++#include <sys/types.h>
+ #include "md5.h"
+ #include "memberlist.h"
+ #include "groupdef.h"
+@@ -2318,10 +2319,8 @@
+     }
+     writeGraphFooter(md5stream);
+     resetReNumbering();
+-    uchar md5_sig[16];
+     QCString sigStr(33);
+-    MD5Buffer((const unsigned char *)theGraph.data(),theGraph.length(),md5_sig);
+-    MD5SigToString(md5_sig,sigStr.data(),33);
++    MD5Data((const unsigned char *)theGraph.data(),theGraph.length(),sigStr.data());
+     bool regenerate=FALSE;
+     if (checkAndUpdateMd5Signature(absBaseName,sigStr) || 
+         !checkDeliverables(absImgName,absMapName))
+@@ -3021,10 +3020,8 @@
+     }
+   }
+   writeGraphFooter(md5stream);
+-  uchar md5_sig[16];
+   QCString sigStr(33);
+-  MD5Buffer((const unsigned char *)buf.data(),buf.length(),md5_sig);
+-  MD5SigToString(md5_sig,sigStr.data(),33);
++  MD5Data((const unsigned char *)buf.data(),buf.length(),sigStr.data());
+   if (reNumber)
+   {
+     resetReNumbering();
+@@ -3895,10 +3892,8 @@
+   QGString theGraph;
+   FTextStream md5stream(&theGraph);
+   m_dir->writeDepGraph(md5stream);
+-  uchar md5_sig[16];
+   QCString sigStr(33);
+-  MD5Buffer((const unsigned char *)theGraph.data(),theGraph.length(),md5_sig);
+-  MD5SigToString(md5_sig,sigStr.data(),33);
++  MD5Data((const unsigned char *)theGraph.data(),theGraph.length(),sigStr.data());
+   bool regenerate=FALSE;
+   if (checkAndUpdateMd5Signature(absBaseName,sigStr) ||
+       !checkDeliverables(format==BITMAP ? absImgName :
+@@ -4025,10 +4020,8 @@
+   md5stream << "  Node18 -> Node9 [dir=\"back\",color=\"darkorchid3\",fontsize=\"" << FONTSIZE << "\",style=\"dashed\",label=\"m_usedClass\",fontname=\"" << FONTNAME << "\"];\n";
+   md5stream << "  Node18 [shape=\"box\",label=\"Used\",fontsize=\"" << FONTSIZE << "\",height=0.2,width=0.4,fontname=\"" << FONTNAME << "\",color=\"black\",URL=\"$classUsed" << Doxygen::htmlFileExtension << "\"];\n";
+   writeGraphFooter(md5stream);
+-  uchar md5_sig[16];
+   QCString sigStr(33);
+-  MD5Buffer((const unsigned char *)theGraph.data(),theGraph.length(),md5_sig);
+-  MD5SigToString(md5_sig,sigStr.data(),33);
++  MD5Data((const unsigned char *)theGraph.data(),theGraph.length(),sigStr.data());
+   QCString absBaseName = (QCString)path+"/graph_legend";
+   QCString absDotName  = absBaseName+".dot";
+   QCString imgExt      = Config_getEnum("DOT_IMAGE_FORMAT");
+@@ -4424,10 +4417,8 @@
+ 
+   writeGraphFooter(md5stream);
+   resetReNumbering();
+-  uchar md5_sig[16];
+   QCString sigStr(33);
+-  MD5Buffer((const unsigned char *)theGraph.data(),theGraph.length(),md5_sig);
+-  MD5SigToString(md5_sig,sigStr.data(),33);
++  MD5Data((const unsigned char *)theGraph.data(),theGraph.length(),sigStr.data());
+   QCString imgExt      = Config_getEnum("DOT_IMAGE_FORMAT");
+   QCString baseName    = m_diskName;
+   QCString imgName     = baseName+"."+imgExt;
diff --git a/devel/doxygen/files/patch-md5-doxygen.pro.in b/devel/doxygen/files/patch-md5-doxygen.pro.in
new file mode 100644
index 000000000000..75ad3757fd2a
--- /dev/null
+++ b/devel/doxygen/files/patch-md5-doxygen.pro.in
@@ -0,0 +1,20 @@
+--- src/doxygen.pro.in-orig	2014-06-11 20:16:21.000000000 +0200
++++ src/doxygen.pro.in	2014-06-11 20:16:59.000000000 +0200
+@@ -18,7 +18,7 @@
+ CONFIG       =	console warn_on $extraopts
+ HEADERS      =	doxygen.h 
+ SOURCES      =	main.cpp 
+-unix:LIBS                  += -L../lib -ldoxygen -ldoxycfg -lqtools -lmd5 -lpthread %%SQLITE3_LIBS%% %%LIBCLANG_LIBS%%
++unix:LIBS                  += -L../lib -ldoxygen -ldoxycfg -lqtools -lmd -lpthread %%SQLITE3_LIBS%% %%LIBCLANG_LIBS%%
+ win32:INCLUDEPATH          += .
+ win32-mingw:LIBS           += -L../lib -ldoxygen -ldoxycfg -lqtools -lmd5 -lpthread -llibiconv -lole32 %%SQLITE3_LIBS%% %%LIBCLANG_LIBS%%
+ win32-msvc:LIBS            += qtools.lib md5.lib doxygen.lib doxycfg.lib shell32.lib iconv.lib
+@@ -29,7 +29,7 @@
+ win32-g++:LIBS             = -L../lib -ldoxygen -ldoxycfg -lqtools -lmd5 -liconv -lpthread %%SQLITE3_LIBS%% %%LIBCLANG_LIBS%% -Wl,--as-needed -lole32
+ win32-g++:TMAKE_CXXFLAGS   += -fno-exceptions -fno-rtti
+ DEPENDPATH                 += ../generated_src/doxygen
+-INCLUDEPATH                += ../qtools ../libmd5 .
++INCLUDEPATH                += ../qtools .
+ DESTDIR                    =  ../bin
+ TARGET                     =  doxygen
+ unix:TARGETDEPS            =  ../lib/libdoxygen.a ../lib/libdoxycfg.a
diff --git a/devel/doxygen/files/patch-md5-memberdef b/devel/doxygen/files/patch-md5-memberdef
new file mode 100644
index 000000000000..86b2ba655836
--- /dev/null
+++ b/devel/doxygen/files/patch-md5-memberdef
@@ -0,0 +1,23 @@
+--- src/memberdef.cpp-orig	2014-06-11 20:17:47.000000000 +0200
++++ src/memberdef.cpp	2014-06-11 20:19:38.000000000 +0200
+@@ -17,6 +17,7 @@
+ #include <qglobal.h>
+ #include <qregexp.h>
+ #include <assert.h>
++#include <sys/types.h>
+ #include "md5.h"
+ #include "memberdef.h"
+ #include "membername.h"
+@@ -3305,11 +3306,9 @@
+   }
+ 
+   // convert to md5 hash
+-  uchar md5_sig[16];
+   QCString sigStr(33);
+-  MD5Buffer((const unsigned char *)memAnchor.data(),memAnchor.length(),md5_sig);
+   //printf("memAnchor=%s\n",memAnchor.data());
+-  MD5SigToString(md5_sig,sigStr.data(),33);
++  MD5Data((const unsigned char *)memAnchor.data(),memAnchor.length(),sigStr.data());
+   m_impl->anc = "a"+sigStr;
+ }
+ 
diff --git a/devel/doxygen/files/patch-md5-membergroup b/devel/doxygen/files/patch-md5-membergroup
new file mode 100644
index 000000000000..189140f5218c
--- /dev/null
+++ b/devel/doxygen/files/patch-md5-membergroup
@@ -0,0 +1,24 @@
+--- src/membergroup.cpp-orig	2014-06-11 20:23:51.000000000 +0200
++++ src/membergroup.cpp	2014-06-11 20:24:25.000000000 +0200
+@@ -28,6 +28,7 @@
+ #include "docparser.h"
+ #include "marshal.h"
+ #include "entry.h"
++#include <sys/types.h>
+ #include "md5.h"
+ 
+ //static QCString idToName(int id)
+@@ -307,12 +308,10 @@
+ 
+ QCString MemberGroup::anchor() const
+ {
+-  uchar md5_sig[16];
+   QCString sigStr(33);
+   QCString locHeader = grpHeader;
+   if (locHeader.isEmpty()) locHeader="[NOHEADER]";
+-  MD5Buffer((const unsigned char *)locHeader.data(),locHeader.length(),md5_sig);
+-  MD5SigToString(md5_sig,sigStr.data(),33);
++  MD5Data((const unsigned char *)locHeader.data(),locHeader.length(),sigStr.data());
+   return "amgrp"+sigStr;
+ }
+ 
diff --git a/devel/doxygen/files/patch-md5-util b/devel/doxygen/files/patch-md5-util
new file mode 100644
index 000000000000..764a835e29fd
--- /dev/null
+++ b/devel/doxygen/files/patch-md5-util
@@ -0,0 +1,48 @@
+--- src/util.cpp-orig	2014-06-11 20:24:54.000000000 +0200
++++ src/util.cpp	2014-06-11 20:26:48.000000000 +0200
+@@ -19,6 +19,7 @@
+ #include <errno.h>
+ #include <math.h>
+ 
++#include <sys/types.h>
+ #include "md5.h"
+ 
+ #include <qregexp.h>
+@@ -5283,16 +5284,16 @@
+     if (resultLen>=128) // prevent names that cannot be created!
+     {
+       // third algorithm based on MD5 hash
+-      uchar md5_sig[16];
+       QCString sigStr(33);
+-      MD5Buffer((const unsigned char *)result.data(),resultLen,md5_sig);
+-      MD5SigToString(md5_sig,sigStr.data(),33);
++      MD5Data((const unsigned char *)result.data(),resultLen,sigStr.data());
+       result=result.left(128-32)+sigStr; 
+     }
+   }
+   if (createSubdirs)
+   {
++#if MAP_ALGO==ALGO_COUNT || MAP_ALGO==ALGO_CRC16
+     int l1Dir=0,l2Dir=0;
++#endif
+ 
+ #if MAP_ALGO==ALGO_COUNT 
+     // old algorithm, has the problem that after regeneration the
+@@ -5323,12 +5324,13 @@
+     l2Dir = (dirNum>>4)&0xff;
+ #elif MAP_ALGO==ALGO_MD5
+     // third algorithm based on MD5 hash
+-    uchar md5_sig[16];
+-    MD5Buffer((const unsigned char *)result.data(),result.length(),md5_sig);
+-    l1Dir = md5_sig[14]&0xf;
+-    l2Dir = md5_sig[15];
++    char md5[33];
++    MD5Data((const unsigned char *)result.data(),result.length(),md5);
++    result.prepend(QCString().sprintf("d%c/d%c%c/",md5[29],md5[30],md5[31]));
+ #endif
++#if MAP_ALGO==ALGO_COUNT || MAP_ALGO==ALGO_CRC16
+     result.prepend(QCString().sprintf("d%x/d%02x/",l1Dir,l2Dir));
++#endif
+   }
+   //printf("*** convertNameToFile(%s)->%s\n",name,result.data());
+   return result;
diff --git a/devel/doxygen/files/patch-refman b/devel/doxygen/files/patch-refman
new file mode 100644
index 000000000000..bdc5f3669407
--- /dev/null
+++ b/devel/doxygen/files/patch-refman
@@ -0,0 +1,31 @@
+--- refman-patch.orig	1970-01-01 01:00:00.000000000 +0100
++++ refman-patch	2014-06-13 22:41:10.000000000 +0200
+@@ -0,0 +1,28 @@
++--- refman.tex-orig	2014-06-12 21:40:19.000000000 +0200
+++++ refman.tex	2014-06-12 21:46:06.000000000 +0200
++@@ -13,6 +13,8 @@
++ \usepackage{textcomp}
++ \usepackage[nointegrals]{wasysym}
++ \usepackage[table]{xcolor}
+++\usepackage{longtable}
+++\usepackage{enumitem}
++ 
++ % Font selection
++ \usepackage[T1]{fontenc}
++@@ -93,7 +95,7 @@
++ % Hyperlinks (required, but should be loaded last)
++ \usepackage{ifpdf}
++ \ifpdf
++-  \usepackage[pdftex,pagebackref=true]{hyperref}
+++  \usepackage[pdftex,unicode,pagebackref=true]{hyperref}
++ \else
++   \usepackage[ps2pdf,pagebackref=true]{hyperref}
++ \fi
++@@ -118,7 +120,6 @@
++ \hypersetup{pageanchor=false,
++              bookmarks=true,
++              bookmarksnumbered=true,
++-             pdfencoding=unicode
++             }
++ \pagenumbering{roman}
++ \begin{titlepage}
diff --git a/devel/doxygen/files/patch-warnings b/devel/doxygen/files/patch-warnings
deleted file mode 100644
index b2e50c9e729b..000000000000
--- a/devel/doxygen/files/patch-warnings
+++ /dev/null
@@ -1,15 +0,0 @@
---- qtools/qgdict.cpp	Wed Apr 13 15:51:44 2005
-+++ qtools/qgdict.cpp	Wed Jun 14 01:43:49 2006
-@@ -41,4 +41,5 @@
- #include "qdatastream.h"
- #include <ctype.h>
-+#include <sys/types.h>
- 
- // NOT REVISED
-@@ -1005,5 +1006,5 @@
- 	    case PtrKey:
- 		{
--		    Q_UINT32 k;
-+		    uintptr_t k;
- 		    s >> k;
- 		    read( s, d );